title: BSCHF_128

description: human whole blood RNA profile


title: BSCHF_132

status: Public on Mar 01 2023

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: human whole blood RNA profile

hyb_protocol: 5 μg of fragmented, end–labelled sense strand target cDNA was hybridized to each array and scanned using a Gene Chip Scanner 30007G

scan_protocol: standard protocol

data_processing: The normalisation used the method by Welsh et al called IRON. BMC Bioinformatics. 2013 May 7;14:153. doi: 10.1186/1471-2105-14-153.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: The RNA was processed to single-stranded sense fragmented DNA using the GeneChip® WT PLUS Reagent Kit which relies on a reverse transcription priming strategy that primes both poly-A and non-poly-A RNA

extract_protocol: PAXgene tubes (Qiagen) and RNA was isolated using TRizol® (Life Technologies) and dissolved in 20 μl RNAse-free water.

tag: tissue

value: whole blood

tag: diagnosis

value: Chronic Heart Failure (CHF)

tag: Sex

value: Male

tag: age


title: BSCHF_129

description: human whole blood RNA profile

value: Female


title: BSCHF_126

description: human whole blood RNA profile


title: BSCHF_127

description: human whole blood RNA profile


title: BSCHF_130

description: human whole blood RNA profile


title: BSCHF_123

description: human whole blood RNA profile


title: BSCHF_122

description: human whole blood RNA profile


title: BSCHF_121

description: human whole blood RNA profile


title: BSCHF_120

description: human whole blood RNA profile


title: BSCHF_125

description: human whole blood RNA profile


title: BSCHF_124

description: human whole blood RNA profile


title: BSCHF_119

description: human whole blood RNA profile


title: BSCHF_118

description: human whole blood RNA profile


title: BSCHF_111

description: human whole blood RNA profile


title: BSCHF_115

description: human whole blood RNA profile


title: BSCHF_113

description: human whole blood RNA profile


title: BSCHF_106

description: human whole blood RNA profile


title: BSCHF_117

description: human whole blood RNA profile


title: BSCHF_100

description: human whole blood RNA profile


title: BSCHF_116

description: human whole blood RNA profile


title: BSCHF_108

description: human whole blood RNA profile


title: BSCHF_103

description: human whole blood RNA profile


title: BSCHF_99

description: human whole blood RNA profile


title: BSCHF_114

description: human whole blood RNA profile


title: BSCHF_105

description: human whole blood RNA profile


title: BSCHF_112

description: human whole blood RNA profile


title: BSCHF_102

description: human whole blood RNA profile


title: BSCHF_97

description: human whole blood RNA profile


title: BSCHF_96

description: human whole blood RNA profile


title: BSCHF_91

description: human whole blood RNA profile


title: BSCHF_104

description: human whole blood RNA profile


title: BSCHF_89

description: human whole blood RNA profile


title: BSCHF_92

description: human whole blood RNA profile


title: BSCHF_90

description: human whole blood RNA profile


title: BSCHF_95

description: human whole blood RNA profile


title: BSCHF_101

description: human whole blood RNA profile


title: BSCHF_94

description: human whole blood RNA profile


title: BSCHF_93

description: human whole blood RNA profile


title: BSCHF_107

description: human whole blood RNA profile


title: BSCHF_109

description: human whole blood RNA profile


title: BSCHF_110

description: human whole blood RNA profile


title: BSCHF_98

description: human whole blood RNA profile


title: BSCHF_88

description: human whole blood RNA profile


title: BSCHF_86

description: human whole blood RNA profile


title: BSCHF_87

description: human whole blood RNA profile


title: BSCHF_81

description: human whole blood RNA profile


title: BSCHF_85

description: human whole blood RNA profile


title: BSCHF_84

description: human whole blood RNA profile


title: BSCHF_82

description: human whole blood RNA profile


title: BSCHF_79

description: human whole blood RNA profile


title: BSCHF_78

description: human whole blood RNA profile


title: BSCHF_77

description: human whole blood RNA profile


title: BSCHF_76

description: human whole blood RNA profile


title: BSCHF_75

description: human whole blood RNA profile


title: BSCHF_80

description: human whole blood RNA profile


title: BSCHF_74

description: human whole blood RNA profile


title: BSCHF_73

description: human whole blood RNA profile


title: BSCHF_68

description: human whole blood RNA profile


title: BSCHF_67

description: human whole blood RNA profile


title: BSCHF_83

description: human whole blood RNA profile


title: BSCHF_71

description: human whole blood RNA profile


title: BSCHF_64

description: human whole blood RNA profile


title: BSCHF_72

description: human whole blood RNA profile


title: BSCHF_65

description: human whole blood RNA profile


title: BSCHF_63

description: human whole blood RNA profile


title: BSCHF_62

description: human whole blood RNA profile


title: BSCHF_59

description: human whole blood RNA profile


title: BSCHF_60

description: human whole blood RNA profile


title: BSCHF_57

description: human whole blood RNA profile


title: BSCHF_70

description: human whole blood RNA profile


title: BSCHF_69

description: human whole blood RNA profile


title: BSCHF_56

description: human whole blood RNA profile


title: BSCHF_58

description: human whole blood RNA profile


title: BSCHF_66

description: human whole blood RNA profile


title: BSCHF_61

description: human whole blood RNA profile


title: BSCHF_54

description: human whole blood RNA profile


title: BSCHF_55

description: human whole blood RNA profile


title: BSCHF_53

description: human whole blood RNA profile


title: BSCHF_52

description: human whole blood RNA profile


title: BSCHF_51

description: human whole blood RNA profile


title: BSCHF_47

description: human whole blood RNA profile


title: BSCHF_46

description: human whole blood RNA profile


title: BSCHF_23

description: human whole blood RNA profile


title: BSCHF_30

description: human whole blood RNA profile


title: BSCHF_37

description: human whole blood RNA profile


title: BSCHF_44

description: human whole blood RNA profile


title: BSCHF_40

description: human whole blood RNA profile


title: BSCHF_27

description: human whole blood RNA profile


title: BSCHF_34

description: human whole blood RNA profile


title: BSCHF_49

description: human whole blood RNA profile


title: BSCHF_33

description: human whole blood RNA profile


title: BSCHF_20

description: human whole blood RNA profile


title: BSCHF_26

description: human whole blood RNA profile


title: BSCHF_41

description: human whole blood RNA profile


title: BSCHF_31

description: human whole blood RNA profile


title: BSCHF_39

description: human whole blood RNA profile


title: BSCHF_38

description: human whole blood RNA profile


title: BSCHF_24

description: human whole blood RNA profile


title: BSCHF_48

description: human whole blood RNA profile


title: BSCHF_45

description: human whole blood RNA profile


title: BSCHF_50

description: human whole blood RNA profile


title: BSCHF_32

description: human whole blood RNA profile


title: BSCHF_25

description: human whole blood RNA profile


title: BSCHF_21

description: human whole blood RNA profile


title: BSCHF_28

description: human whole blood RNA profile


title: BSCHF_35

description: human whole blood RNA profile


title: BSCHF_42

description: human whole blood RNA profile


title: BSCHF_43

description: human whole blood RNA profile


title: BSCHF_19

description: human whole blood RNA profile


title: BSCHF_22

description: human whole blood RNA profile


title: BSCHF_29

description: human whole blood RNA profile


title: BSCHF_36

description: human whole blood RNA profile


title: BSCHF_15

description: human whole blood RNA profile


title: BSCHF_16

description: human whole blood RNA profile


title: Spaceflight mouse 3 - F13

type: SRA

city: Loma Linda

first: Lorelei

last: Hughes

state: CA

address: 11021 Campus

department: Pathology and Human Anatomy

country: USA

institute: Loma Linda University

library_source: transcriptomic

data_processing:
Cutadapt and perl scripts in house were used to remove reads with adaptor contamination, low quality bases and undetermined bases
sequence quality verified using FastQC
HISAT2 was used to map the reads
StringTie was used to assemble mapped reads
StringTie and Ballgown were used to estimate expression levels of transcripts
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method

value: heart

value: female

value: 14 weeks

tag: treatment

value: spaceflight

tag: time

value: 30 days


title: BSCHF_12

description: human whole blood RNA profile


title: BSCHF_9

description: human whole blood RNA profile


title: Spaceflight mouse 2 - F12


title: BSCHF_17

description: human whole blood RNA profile


title: Spaceflight mouse 1 - F11


title: BSCHF_10

description: human whole blood RNA profile


title: BSCHF_14

description: human whole blood RNA profile


title: BSCHF_5

description: human whole blood RNA profile


title: BSCHF_8

description: human whole blood RNA profile


title: BSCHF_6

description: human whole blood RNA profile


title: BSCHF_13

description: human whole blood RNA profile


title: BSCHF_7

description: human whole blood RNA profile


title: BSCHF_18

description: human whole blood RNA profile


title: singleBetaCells_WT_spheroids_rep1

status: Public on Feb 16 2023

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

description:
EpM196_plate1
total_cells_metadata.csv
total_cells_counts.csv

library_source: transcriptomic single cell

data_processing:
Paired end reads were processed using scRNA-seq function in snakePipes (Bhardwaj et al., 2019) (v1.3.0). Briefly, cell barcodes and UMI’s from read 1 were moved into the header of read2 that was then trimmed for adaptors and polyAs using cut adapt (v2.1).
The subsequent alignment to the mm10 reference genome (GRCm38) was performed using STAR (v2.4.2a).
Raw counts are extracted using feature counts (v1.6.4) using gene annotation version M9 of gencode, and pseudogenes were removed.
Data were analyzed using the Seurat v4 algorithm (Stuart et al., 2019), which was followed by standard preprocessing. In brief, cell filtration threshold was set to unique 876 feature counts >700 and >40% mitochondrial genes for SCAN-seq.
After QC filtering, the data were normalized by employing a global-scaling normalization method 878 that normalizes the feature expression measurements for each cell by the total expression, multiples the results by 10000 and log-transforms the product. Highly variable transcripts were identified using the Seurat4 FindVaribleFeatures function. The data were scaled while batch correction was applied using the vars.to.regress option to provide an equal weight in downstream analysis and buffer the noise of highly-expressed genes. Then, linear dimensional reduction was applied on the scaled data.
Assembly: GRCm38/mm10
Supplementary files format and content: total_cells_metadata.csv; tab-delimited file with information on cell IDs, barcoding, and additional covariates, for each single cell profiled
Supplementary files format and content: total_cells_counts.csv; tab-delimited file with raw counts for each cell ID and each gene identifier
Supplementary files format and content: total_cells_FACS_counts.csv; tab-delimited file with scaled FACS counts for each cell ID and each feature analyzed by FACS

source_name: Pancreatic islets

growth_protocol: All animals were maintained on a normal chow diet with 15% fat (Ssniff GmbH), fed ad libitum with free access to water (HCl acidified, pH 2.5-3) under controlled humidity and temperature with a 12-hour light and 12-hour dark cycle. All animal studies were performed with the approval of the local authority (Regierungspräsidium Freiburg, Germany) under license number 35-9185.81/G-16/120.

extract_protocol:
The new multi-modal ‘single cell Surface, Cytoplasmic And Nuclear staining and RNA sequencing (SCAN-seq) of FACS labeled and fixed single β-cells (described above) was built off of the CEL-Seq2 method(Hashimshony et al., 2016; Lu et al., 2018). Insulin positive cells were index-sorted into 384 well plates containing 384 unique barcodes, Single cells were sorted in 384-well plates (Bio-Rad Laboratories,HSP3801) containing lysis buffer and mineral oil (Sigma, M8410) using BD FACS Aria FUSION. The sorter was run on single-cell sort mode with index sorting. Doublets were excluded using pulse geometry gates (FSC-W × FSC-H and SSC-W × SSC-H). Importantly, cells from all conditions/biological replicates were equally distributed into wells of all sorted plates from the same experiment to enable optimal batch correction in case of evident plate bias in the protein of transcriptional data. After the completion of sorting, the plates were centrifuged for 2 minutes at 2,200 g at 4°C, snap-frozen in liquid nitrogen and stored at -80C for up to two weeks until processed.
160 nL of reverse transcription reaction mix and 2.2 mL of second strand reaction mix was used to convert RNA into cDNA. cDNA from 384- cells was pooled together before the clean-up and in vitro transcription, generating one library from one 384-well plate. 0.8 mL of AMPure/RNAClean XP beads (Beckman Coulter GmbH, Germany) per 1 mL of sample were used during all the purification steps including library cleanup. Libraries were sequenced on a single lane (pair-end multiplexing run, 100 bp read length) of an Illumina HiSeq system targeting 200,000 reads per cell.

treatment_protocol: Adult pancreata were perfused through the common bile duct using a 30-gauge needle with Collagenase 4 solution (dissolved in 1x HBSS, 10mM HEPES at a concentration of 1mg per mL), this step was excluded for neonatal islet isolation. Then the pancreata were dissected and incubated 30 minutes in the same collagenase solution. Islets were purified as previously described(Dror et al., 2017). The Isolated islets were hand-picked and cultured in complete media (RMPI-1640 containing 11 mM glucose, 10% FBS, 0.1% Penicillin/Streptomycin, gentamicin and Amphotericin B; Thermo Fisher) and maintained at 37°C in 5% CO2 environment to allow their recovery. For islet dispersion, islets were incubated in accutase for 4 minutes at 37°C, then gently pipetted using a 1mL pipette for 20 times. Immediately after, single cell suspensions were examined under the microscope, and validated cell suspensions were washed with 2mL of ice cold FACS buffer (PBS, 0.5% BSA, 5mM EDTA) or ice-cold PBS (in case of subsequent fixable viability labeling; 5 minutes zombie dye on ice). Cell surface CD24 (mouse: Thermo Fisher 48-0242-82, human: Biologend, 311122 ,1:250), CD45 (Thermo Fisher, 11-0451-82, 1:200), and CD31 (BD pharminfen, 558738 1:200) labeling was done for 30 minutes on ice (diluted in FACS buffer). After washing, cells were fixed in 1% methanol free formaldehyde (Thermo fisher, 28906, 1mL; diluted in RPMI; freshly made) for 15 minutes, the reaction was quenched with glycine (end conc. of 125mM) and cells were washed with additional 1mL of FACS buffer. Intracellular labeling of insulin (sc-8033, 1:100), glucagon (sc-51459, 1:100), somatostatin (sc-55565, 1:100), pancreatic polypeptide (sc-514155, 1:100), MKI67 (47-5698-82, 1:200), TOM20 (Abcam, 1:500), and chromatin labeling using conjugated H3K27me3 (Origene, TA347154 conjugated using mix-n-stain CF555 kit, Sigma), H3K4me3 (C15410003, conjugated using mix-n-stain CF405 kit, Sigma), H3K36me3 (C15410192, conjugated using mix-n-stain CF405 kit, Sigma), H3K9me3 (C15410193, conjugated using mix-n-stain CF488 kit, Sigma), H3K27ac (C15410196, conjugated using mix-n-stain CF488 kit, Sigma) at final concentrations of 5ug/ml, was done in permeabilization buffer (eBioscience, 00-8333-56). For data in Figure 1A, H3K27me3 was labeled together with either H3K9me3 and H3K36me3 or H3K27ac and H3K4me3. The presented data in Figure S1F shows additional labeling with H3K27me3 (C15410195, Diagenode). Unless stated differently insulin positive β-cells were analyzed and sorted while excluding glucagon, somatostatin, pancreatic polypeptide, CD31, and CD45 positive cells that were included in a ‘dump channel'; 488, which contained all of the antibodies that are specific for the unwanted cells. Washing between steps was determined differently; live cells were centrifuged at 190g, fixed cells at 350g and fixed-permeabilized cells were centrifuged at 500g, all for 4min at 4 degrees.

value: Pancreatic islets

tag: strain

tag: cell type

value: pancreatic beta cells

tag: genotype

value: WT

value: 24 weeks


title: singleBetaCells_EedHet-WT_rep4

description:
EpM190_plate4
total_cells_metadata.csv
total_cells_counts.csv

value: EedHet and WT


title: singleBetaCells_EedHet-WT_rep3

description:
EpM190_plate3
total_cells_metadata.csv
total_cells_counts.csv


title: singleBetaCells_EedHet-WT_rep5

description:
EpM190_plate5
total_cells_metadata.csv
total_cells_counts.csv


title: singleBetaCells_EedHet-WT_rep2

description:
EpM190_plate2
total_cells_metadata.csv
total_cells_counts.csv


title: singleBetaCells_EedHet-WT_rep1

description:
EpM190_plate1
total_cells_metadata.csv
total_cells_counts.csv


title: singleBetaCells_WT_rep6

description:
EpM142_plate6
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv

value: 12 weeks


title: singleBetaCells_WT_rep3

description:
EpM142_plate3
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: singleBetaCells_WT_rep4

description:
EpM142_plate4
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: singleBetaCells_WT_rep2

description:
EpM142_plate2
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: singleBetaCells_WT_rep5

description:
EpM142_plate5
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: singleBetaCells_WT_rep1

description:
EpM142_plate1
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: singleBetaCells_EedHet-WT_rep6

description:
EpM190_plate6
total_cells_metadata.csv
total_cells_counts.csv


title: BSCHF_3

description: human whole blood RNA profile


title: singleBetaCells_EedHet-EedKO-WT_rep2

description:
EpM135_plate2
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv

value: EedHet, EedKO and WT

value: 10 weeks


title: singleBetaCells_EedHet-EedKO-WT_rep1

description:
EpM135_plate1
total_cells_metadata.csv
total_cells_counts.csv
total_cells_FACS_counts.csv


title: MMC+oBHV replicate 1

status: Public on Feb 17 2023

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

hyb_protocol: Fragmented sample was hybridized to Affymetrix Clariom S arrays at 45 °C overnight.

scan_protocol: Arrays were imaged using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data was analyzed using the Transcriptome Analysis Console software, Thermo Fischer. Data was processed using RMA, Quantile Normalization, HDF5 output.

label: Biotin

source_name: B16-C10 subcutaneuos tumour from C57Bl/6 mouse

label_protocol: RNA was normalized to an input amount of 100 ng and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG

growth_protocol: 6- to 8-week-old C57Bl/6 mice were subcutaneously implanted with 5 × 106 B16-C10 cells resuspended in 200 µL PBS into the left flank

extract_protocol: Mice were sacrificed and tumours harvested at day 5. Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purifying using the Qiagen RNA extraction kit (Cat #74004)

treatment_protocol: At 2 weeks post-injection: for MMC therapy, tumors were treated intratumorally (i.t.) with 100 µg MMC in 50 µL sterile water only at day 1. For oBHV therapy, tumors were treated i.t. by injecting 2 × 107 pfu oBHV in 50 μL PBS beginning at day 2 once daily for 3 consecutive days (days 2, 3 and 4)

value: B16-C10 subcutaneuos tumour

value: MMC+oBHV


title: BSCHF_4

description: human whole blood RNA profile

value: whole blood

value: Chronic Heart Failure (CHF)

value: Male


title: betaCell_beta-LO_rep9

data_processing:
RNA-seq was performed with at least three independent biological replicates. Raw sequences from the biological replicates were aligned. Reads for mouse bulk RNA-seq datasets were mapped against mouse genome version mm10 with the snakePipes2 RNA-seq pipeline.
Differential expression analysis was performed with DEseq2 (Love et al., 2014). Genes with counts <2 were excluded from differential analysis. Differential genes were called with an FDR threshold of 0.05 and a fold change of 1.33. After QC, and exclusion of lowly expressed genes (>2 counts) differential expression of the raw counts was performed using DESeq2 v1.34.1.
Samples were batch-corrected using Limma and normalized count matrices were inspected using PCA.
Gene Set Enrichment Analysis (GSEA) of DE results was performed with fgsea R-package.
Enrichment maps were generated in Cytoscape (Shannon et al., 2003).
Assembly: GRCm38/mm10
Supplementary files format and content: H3K27me3HI-H3K27me3LO_counts_matrix.csv; .csv reporting raw counts from all H3K27me3-HI/-LO sorted beta cells' replicates.
Supplementary files format and content: beta-HI-beta-LO_counts_matrix.csv; .csv reporting raw counts from all beta-HI/-2 sorted beta cells' replicates.

extract_protocol:
Total RNA from 1,000 H3K27me3 HI/LO β-cells or from 50,000 sorted beta-HI/2 β-cells was extracted using the miRNeasy FFPE Kit (QIAGEN, 217504)
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (E6420L). Library fragments of 350 ± 20 bp were obtained, and the quality was assessed using a Fragment Analyzer (Advanced Analytical).

treatment_protocol: Adult pancreata were perfused through the common bile duct using a 30-gauge needle with Collagenase 4 solution (dissolved in 1x HBSS, 10mM HEPES at a concentration of 1mg per mL), this step was excluded for neonatal islet isolation. Then the pancreata were dissected and incubated 30 minutes in the same collagenase solution. Islets were purified as previously described(Dror et al., 2017). The Isolated islets were hand-picked and cultured in complete media (RMPI-1640 containing 11 mM glucose, 10% FBS, 0.1% Penicillin/Streptomycin, gentamicin and Amphotericin B; Thermo Fisher) and maintained at 37°C in 5% CO2 environment to allow their recovery. For islet dispersion, islets were incubated in accutase for 4 minutes at 37°C, then gently pipetted using a 1mL pipette for 20 times. Immediately after, single cell suspensions were examined under the microscope, and validated cell suspensions were washed with 2mL of ice cold FACS buffer (PBS, 0.5% BSA, 5mM EDTA) or ice-cold PBS (in case of subsequent fixable viability labeling; 5 minutes zombie dye on ice). Cell surface CD24 (mouse: Thermo Fisher 48-0242-82, human: Biologend, 311122 ,1:250), CD45 (Thermo Fisher, 11-0451-82, 1:200), and CD31 (BD pharminfen, 558738 1:200) labeling was done for 30 minutes on ice (diluted in FACS buffer). After washing, cells were fixed in 1% methanol free formaldehyde (Thermo fisher, 28906, 1mL; diluted in RPMI; freshly made) for 15 minutes, the reaction was quenched with glycine (end conc. of 125mM) and cells were washed with additional 1mL of FACS buffer. Intracellular labeling of insulin (sc-8033, 1:100), glucagon (sc-51459, 1:100), somatostatin (sc-55565, 1:100), pancreatic polypeptide (sc-514155, 1:100), MKI67 (47-5698-82, 1:200), TOM20 (Abcam, 1:500), and chromatin labeling using conjugated H3K27me3 (Origene, TA347154 conjugated using mix-n-stain CF555 kit, Sigma), H3K4me3 (C15410003, conjugated using mix-n-stain CF405 kit, Sigma), H3K36me3 (C15410192, conjugated using mix-n-stain CF405 kit, Sigma), H3K9me3 (C15410193, conjugated using mix-n-stain CF488 kit, Sigma), H3K27ac (C15410196, conjugated using mix-n-stain CF488 kit, Sigma) at final concentrations of 5ug/ml, was done in permeabilization buffer (eBioscience, 00-8333-56). For data in Figure 1A, H3K27me3 was labeled together with either H3K9me3 and H3K36me3 or H3K27ac and H3K4me3. The presented data in Figure S1F shows additional labeling with H3K27me3 (C15410195, Diagenode). Unless stated differently insulin positive β-cells were analyzed and sorted while excluding glucagon, somatostatin, pancreatic polypeptide, CD31, and CD45 positive cells that were included in a ‘dump channel'; 488, which contained all of the antibodies that are specific for the unwanted cells. Washing between steps was determined differently; live cells were centrifuged at 190g, fixed cells at 350g and fixed-permeabilized cells were centrifuged at 500g, all for 4min at 4 degrees. For experiments with subsequent extraction of RNA, all the steps were done in the presence of RNase inhibitor (recombinant RNasein, Promega, N2511) diluted 1:4,000 for washing steps or 1:400 for incubation while staining and for buffers in the tubes containing the sorted cells followed by snap freeze and storage at –80°C.

tag: cell subtype

value: beta-LO

value: wild type


title: BSCHF_11

description: human whole blood RNA profile


title: betaCell_beta-LO_rep8


title: MMC+oBHV replicate 5


title: PBS replicate 1

value: PBS


title: MMC+oBHV replicate 2


title: betaCell_beta-LO_rep7


title: BSCHF_2

description: human whole blood RNA profile


title: betaCell_beta-LO_rep6


title: PBS replicate 4


title: MMC+oBHV replicate 4


title: PBS replicate 3


title: MMC+oBHV replicate 3


title: BSCHF_1

description: human whole blood RNA profile


title: betaCell_beta-LO_rep5


title: betaCell_beta-LO_rep4


title: betaCell_beta-LO_rep3


title: PBS replicate 2


title: betaCell_beta-LO_rep1


title: PBS replicate 5


title: betaCell_beta-LO_rep2


title: betaCell_beta-HI_rep6

value: beta-HI


title: betaCell_beta-HI_rep5

value: Pancreatic islets


title: betaCell_beta-HI_rep2

value: pancreatic beta cells


title: betaCell_beta-HI_rep3


title: betaCell_beta-HI_rep1


title: betaCell_H3K27me3-LO_4weeks_rep4

value: 4 weeks


title: betaCell_H3K27me3-LO_4weeks_rep3


title: betaCell_H3K27me3-LO_4weeks_rep2


title: betaCell_H3K27me3-LO_10weeks_rep4


title: betaCell_H3K27me3-LO_4weeks_rep1


title: betaCell_H3K27me3-LO_10weeks_rep3


title: betaCell_H3K27me3-LO_10weeks_rep2


title: betaCell_beta-HI_rep4


title: betaCell_H3K27me3-HI_4weeks_rep4


title: betaCell_H3K27me3-HI_4weeks_rep3


title: betaCell_H3K27me3-LO_10weeks_rep1


title: betaCell_H3K27me3-HI_10weeks_rep4


title: betaCell_H3K27me3-HI_10weeks_rep1


title: betaCell_H3K27me3-HI_10weeks_rep2


title: betaCells_beta-LO_rep9

type: genomic

description:
206522590021_R06C02
wild type pancreatic β-cell

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged on the iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v.2011.1 and SeSAMe

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from FACS sorted β-cell

label_protocol: Standard Illumina Infinium HD Assay Methylation Protocol document #15019519 v01

growth_protocol: Wild-type C57Bl6/J male mice ages 9-12w were used for this study. Pancreatic islets were isolated from the animals post-CO2 euthanisia by pancreatic perfusion with Collagease 4 solution followed by pancreatic disection and incubation at 37 degrees in the Collagease 4 solution. The islets were purified as previously described (Dror et al. 2017), breifly, pancreatic tissue was homogenized and the digestion was quenched using a 0.5% BSA solution (0.5% BSA in 1X HBSS with 24mM HEPES) followed by centrifugation at 200 x g at 4 degrees C for 2 minutes and another wash with 0.5% BSA solution was repeated. The cell suspension was passed through a 420 micron filter and the flow through was pass through an inverted 70 micron filter where the islets were collected and then culured overnight to allow cell recovery at 37 degrees C, 20% C2 and 5% CO2 in compete medium (RPMI-1640 containing 11mM glucose, 10% FBS, 0.1% Penicillin/Streptomycin, Gentamycin, and Amphotericin B).

extract_protocol: The genomic DNA was extracted and purified from all samples using the Zymo Research Quick-DNA Microprep Plus Kit according to standard instructions.

treatment_protocol: The following day after isolation, FACS was performed to sort CD24-positive and -negative beta-cells. Islets were dispersed by a 4 minute incubation in accutase at 37 degrees C followed by a PBS wash and incubation with Zombie Dye (viability stain) on ice for 10 minutes. Cells were washed with 0.5% BSA solution then incubated with anti-CD24 (Thermofisher, 11-0451-82, 1:200) for 30 minutes on ice, followed by a wash and then fixation for 15 minutes in 1% methanol free formaldehyde diluted in RPMI and quenched with glycine (end conc. of 125 mM). Intracellular staining solution containing  anti-Insulin (sc-8022, 1:100), anti-Somatostatin (sc-55565, 1:100) and anti-H3K27Me3 (C15410003, conjugated using mix-n-stain CF405 kit, Sigma) was prepared in permeablization buffer (ebioscience, 00-8333-56) and incubated with the cells on ice for 30 minutes. Cells were washed then resuspended in 0.5% BSA solution followed by cell sorting using a BD FACSymphony S6.

value: male


title: betaCell_H3K27me3-HI_4weeks_rep2


title: betaCell_beta-HI_H3K4me3

library_source: genomic

data_processing:
Data were processed and analyzed using snakePipes 2.5 (Bhardwaj et al., 2019) ‘DNA-mapping’ and ‘ChIPseq’ pipelines.
Reads were trimmed and quality controlled using Cutadapt, and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), respectively.
Mouse reads were mapped with Bowtie2 (Langmead 840 and Salzberg, 2012) on GRCm38/mm10 genome. High quality (MAPQ>3) and properly paired mapped reads were filtered for optical/PCR duplicates using samtools view (Danecek et al., 2021).
Coverage tracks for visualization in IGV or UCSC genome browsers were created with the DeepTools (Ramirez et al., 2016) v3.3.2 command ‘bamCoverage’ and normalized to sequencing depth.
Heatmap visualizations and profile plots of coverage signals over specific regions were generated using the DeepTools commands ‘computeMatrix’, ‘plotHeatmap’ and ‘plotProfile’.
Assembly: GRCm38/mm10
Supplementary files format and content: individual bigWig files reporting the indicated signal coverage for all samples

extract_protocol:
For ChIP-seq experiments: chromatin from snap-frozen pellets of the sorted β- cells were prepared using the NEXSON procedure(Arrigoni et al., 2016) to a 100-800 bp fragment size distribution. Sheared chromatin was controlled for size distribution and cell number. For this, 2 ml of 20 mg/ml Proteinase K was added to a small chromatin aliquot (5 ml) of each sample. Volumes were adjusted to 20 ml using buffer EB (Qiagen). Samples were then reverse-crosslinked by incubating them at 50 °C for 30 min, followed by incubation at 65 °C for 30 min. DNA concentration was measured using Qubit dsDNA HS assay to estimate cell concentration (one mouse diploid cell contains approx. 6.6 pg of DNA). Samples were then purified using Qiagen MinElute columns, and DNA fragment size distribution was checked by capillary electrophoresis (Agilent Fragment Analyzer). For RELACS experiments: the H3K4me3 ChIP-seq was performed using RELACS as previously described (Arrigoni et al., 2018). Briefly, 50,000 beta-HI and-2 cells were thawed in RELACS lysis buffer (10 mM Tris-HCl [pH 8], 10 mM NaCl, 0.2% Igepal, 1× Protease inhibitor cocktail) and the nuclei were isolated by sonication using the NEXSON procedure (Arrigoni et al., 2016). To digest the chromatin, 25 μl of 10× CutSmart buffer (NEB), 2.5 μl 100× Protease inhibitor cocktail and 1 μl of CviKI-1 (5 U/100,000 nuclei, NEB R0710S) were added. The digestion reaction was incubated overnight at 20 °C. End repair and A-tailing was performed and customized adapters were ligated to the fragments. Once barcoded, the samples were pooled together. Chromatin was then sheared by sonication (Covaris E220, MicroTubes, 5 min, peak power 105, duty factor 2, cycles burst 200). This chromatin was used for automated ChIP (Diagenode, C15410003) with the IP-Star Diagenode system.
For ChIP-seq experiments: before ChIP all chromatins were normalized to the same cell number using shearing buffer. Normalized chromatins have been diluted 1:2 in 1X Buffer iC1 (supplemented withprotease inhibitor cocktail) from the Diagenode iDeal ChIP-seq kit for histones (C01010173). Each chromatin sample containing about 6,000 cells was incubated with 1μg of anti-H3K27me3 antibody (Diagenode, C15410195, lot. A1811-001P). ChIP was performed using the automated platform SX-8G IP-Star platform (Diagenode) under the program “ChIP indirect method”. The antibody-chromatin incubation lasted 10h, followed by 3 h percent of the original chromatin was used as input. After the DNA elution, ChIP and input samples were de-crosslinked and purified using the Qiagen MinElute columns. Libraries were prepared on an automated liquid handler (Biomek i7) using the NEBNext Ultra II DNA library preparation kit (NEB, E7645), according to the manufacturer’s instructions and without size selection. For RELACS experiments:  IPs and Inputs were decrosslinked, DNA was purified and libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S and E6440) following the manufacturer’s instructions. Integrity and size-distribution of the samples was assessed before and after library preparation by running on Fragment Analyzer (Advanced Analytical).

tag: chip antibody

value: H3K4me3 (Diagenode, C15410003)


title: betaCell_beta-LO_H3K4me3


title: betaCell_H3K27me3-HI_4weeks_rep1


title: betaCell_beta-LO_H3K27me3_rep3


title: betaCell_beta-HI_H3K27me3_rep3


title: betaCell_beta-HI_input_rep2


title: betaCell_beta-HI_Input


title: betaCell_beta-LO_H3K27me3_rep2


title: betaCell_beta-HI_input_rep1


title: betaCell_beta-LO_H3K27me3_rep1


title: betaCells_beta-HI_rep6

description:
206522590021_R03C01
wild type pancreatic β-cell


title: betaCell_beta-LO_Input


title: betaCell_H3K27me3-HI_10weeks_rep3


title: betaCell_beta-LO_input_rep3


title: betaCell_beta-LO_input_rep2


title: betaCell_beta-LO_input_rep1


title: betaCells_beta-HI_rep8

description:
206522590021_R04C01
wild type pancreatic β-cell


title: betaCells_beta-HI_rep9

description:
206522590021_R04C02
wild type pancreatic β-cell


title: betaCells_beta-HI_rep7

description:
206522590021_R03C02
wild type pancreatic β-cell


title: betaCells_beta-LO_rep8

description:
206522590021_R06C01
wild type pancreatic β-cell


title: betaCells_beta-HI_rep5

description:
206522590021_R02C01
wild type pancreatic β-cell


title: TDPPS920025

status: Public on Nov 01 2022

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description:
RAW_COUNTS_Abnormal-AML-50bp.txt
VOOM_LOG2_CPM_Abnormal-AML-50bp.txt

data_processing:
In house BISR RNASeq workflow
trim all reads to 50bp using hisat2.1.0 (--trim3 100- read length50bp)
map all trimmed reads to human Grch38/hg38 genome using hisat softaware version 2.1.0
Raw read counts are exttracted using software tool featureCounts/subread1.5.1
All raw read counts are normalized using log2 CPM and limma voom transformation
Assembly: Grch38/hg19
Supplementary files format and content: Tab limited txt file that contain raw read counts for each sample
Supplementary files format and content: Tab limited txt file that contain normalized counts for each sample

source_name: blood or bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.

tag: race

value: White

value: Adverse

value: blood or bone marrow

value: Middle


title: TDPPS920197

value: female

value: High


title: betaCells_beta-HI_rep1

description:
206522590020_R03C01
wild type pancreatic β-cell


title: betaCells_beta-LO_rep6

description:
206522590021_R02C02
wild type pancreatic β-cell


title: TDPPS930024


title: TDPPS920259

value: Favorable


title: TDPPS910112

value: Asian


title: TDPPS900196


title: betaCells_beta-HI_rep4

description:
206522590021_R01C01
wild type pancreatic β-cell


title: TDPPS920022


title: betaCells_beta-LO_rep5

description:
206522590021_R01C02
wild type pancreatic β-cell

value: beta-LO


title: betaCells_beta-LO_rep4

description:
206522590020_R06C01
wild type pancreatic β-cell


title: TDPPS900100

value: Intermediate


title: betaCell_beta-HI_H3K27me3_rep1

value: wild type

value: 10 weeks


title: betaCell_beta-HI_H3K27me3_rep2

value: Pancreatic islets

value: beta-HI


title: TDPPS920020


title: TDPPS900045


title: betaCells_beta-LO_rep3

description:
206522590020_R02C01
wild type pancreatic β-cell

value: pancreatic beta cells


title: TDPPS900181

value: male


title: TDPPS920042


title: TDPPS890178


title: betaCells_beta-HI_rep2

description:
206522590020_R04C01
wild type pancreatic β-cell


title: TDPPS890225


title: TDPPS890147


title: betaCell_beta-HI_input_rep3


title: betaCells_beta-LO_rep7

description:
206522590021_R05C01
wild type pancreatic β-cell


title: TDPPS890081


title: TDPPS880353


title: betaCells_beta-LO_rep1

description:
206522590020_R01C01
wild type pancreatic β-cell


title: TDPPS880166

value: Low


title: betaCells_beta-LO_rep2

description:
206522590020_R01C02
wild type pancreatic β-cell


title: TDPPS880074

value: White


title: TDPMT62100


title: betaCells_beta-HI_rep3

description:
206522590020_R05C01
wild type pancreatic β-cell


title: TDPPS880005


title: TDPMT60100


title: TDPPS870166


title: TDPMT43100


title: TDPPS880020

value: Black

value: Adverse


title: TDPMT52100

value: blood or bone marrow


title: TDPC992302

value: female


title: TDPC992295


title: TDPPS880345

value: Middle


title: TDPC992019


title: TDPPS890043

value: High


title: TDPC992269

value: Favorable


title: TDPC991700


title: TDPC991808


title: TDPC991483

value: Hispanic


title: TDPC991925


title: TDPC991430


title: TDPC991422


title: TDPC991242


title: TDPC991679


title: TDPC991225


title: TDPPS870040


title: TDPC991186


title: TDPC991076


title: TDPC990901


title: TDPC990899


title: TDPC990920


title: TDPC990740


title: TDPC990771

value: Intermediate


title: TDPC990720


title: TDPC990596


title: TDPC990501


title: TDPC990649


title: TDPC990383


title: TDPC990309

value: Asian


title: TDPC990135


title: TDPC990269


title: TDPC990123


title: TDPPS890183


title: TDPC990028


title: TDPC981336


title: TDPC990033


title: TDPC981368


title: TDPC981209


title: TDPC981029


title: TDPC981112


title: TDPC981065


title: TDPC990810


title: TDPC980925


title: TDPC980681


title: TDPC980900


title: TDPC980675


title: TDPC980665


title: TDPC980634


title: TDPC980561


title: TDPC981295


title: TDPC980534


title: TDPC980520


title: TDPC980438


title: TDPC980615


title: TDPC980355


title: TDPC980383


title: TDPC981247


title: TDPC980659


title: TDPC980941


title: TDPC980412


title: TDPC980257


title: TDPC980131


title: TDPC981022


title: TDPC980053


title: TDPC970592


title: TDPC970638


title: TDPC970419


title: TDPC970196


title: TDPC970228


title: TDPC970060


title: TDPC96612


title: TDPC980826


title: TDPC970222.v2


title: TDPC96437


title: TDPC970222


title: TDPC96154


title: TDPC95248


title: TDPC96117


title: TDPC95348


title: TDPC95240


title: TDPC95445


title: TDPC95316


title: TDPC95175


title: TDPC980328


title: TDPC95150


title: TDPC95074


title: TDPC95068


title: TDPC95065


title: TDPC95058

value: Other


title: TDPC950150


title: TDPC94009


title: TDPC94046


title: TDPC940055


title: TDPC93191


title: TDPC93307


title: TDPC95054


title: TDPC930235


title: TDPC930127


title: TDPC131259


title: TDPC126706


title: TDPC130870


title: TDPC124122


title: TDPC930172


title: TDPC124264


title: TDPC123596


title: TDPC122483


title: TDPC121118


title: TDPC112488


title: TDPC120698


title: TDPC113217


title: TDPC111953


title: TDPC115180


title: TDPC120860


title: TDPC105054


title: TDPC106633


title: TDPC104063


title: TDPC103925


title: TDPC104000


title: TDPC103906


title: TDPC102657


title: TDPC103069


title: TDPC102124


title: TDPC101528


title: TDPC102937


title: TDPC102383


title: TDPC103019


title: TDPC103113


title: TDPC102198


title: TDPC102143


title: TDPC102170


title: TDPC100820

value: Native Hawaiian


title: TDPC100301


title: TDPC100190


title: TDPC096166


title: TDPC095853


title: TDPC095963


title: TDPC100494


title: TDPC095959


title: TDPC100255


title: TDPC095730


title: TDPC095381


title: TDPC095395


title: TDPC095462


title: TDPC125331


title: TDPC100997


title: TDPC095134


title: TDPC102249


title: TDPC094522


title: TDPC094511


title: TDPC094606


title: TDPC095083


title: TDPC095314


title: TDPC094696


title: TDPC094827


title: TDPC094414


title: TDPC100228


title: TDPC095665


title: TDPC093986


title: TDPC094263


title: TDPC092877


title: TDPC092492


title: TDPC093518


title: TDPC093483


title: TDPC092717


title: TDPC093149


title: TDPC092697


title: TDPC092824


title: TDPC092394


title: TDPC095341


title: TDPC092311


title: TDPC092238


title: TDPC092073


title: TDPC094460


title: TDPC091906


title: TDPC091619


title: TDPC093806


title: TDPC091608


title: TDPC091440


title: TDPC091203


title: TDPC091109


title: TDPC092414


title: TDPC091073


title: TDPC090860


title: TDPC091064


title: TDPC090735


title: TDPC090453


title: TDPC090625


title: TDPC090628


title: TDPC090077


title: TDPC090143


title: TDPC090184


title: TDPC083504


title: TDPC083507


title: TDPC083381


title: TDPC083337


title: TDPC083192


title: TDPC083203


title: TDPC091580


title: TDPC083187


title: TDPC083149


title: TDPC082789


title: TDPC082801


title: TDPC082678


title: TDPC082660


title: TDPC082671


title: TDPC091428


title: TDPC082561


title: TDPC082325


title: TDPC082474


title: TDPC082225


title: TDPC082305


title: TDPC082068


title: TDPC082091


title: TDPC082093


title: TDPC081762


title: TDPC081348


title: TDPC081543


title: TDPC081248


title: TDPC081190


title: TDPC081084


title: TDPC081021


title: TDPC081064


title: TDPC080926


title: TDPC082767


title: TDPC080825


title: TDPC080896


title: TDPC080785


title: TDPC080545


title: TDPC080530


title: TDPC080503


title: TDPC080430


title: TDPC080392


title: TDPC080516


title: TDPC080198


title: TDPC080148


title: TDPC080186


title: TDPC081656


title: TDPC073822


title: TDPC073681


title: TDPC073545


title: TDPC073398


title: TDPC073354


title: TDPC073198


title: TDPC073301


title: TDPC072699


title: TDPC072538


title: TDPC072203


title: TDPC072293


title: TDPC071640


title: TDPC071479


title: TDPC071563


title: TDPC064775


title: TDPC070736


title: TDPC070205


title: TDPC071014

value: Native American


title: TDPC064642


title: TDPC062480


title: TDPC073719


title: TDPC064532


title: TDPC062567


title: TDPC062379


title: TDPC061702


title: TDPC062180


title: TDPC060850


title: TDPC072339


title: TDPC060734


title: TDPC060333


title: TDPC060776


title: TDPC072015


title: TDPC060331


title: TDPC072374


title: TDPC054500


title: TDPC071825


title: TDPC054471


title: TDPC054372


title: TDPC054307


title: TDPC054213


title: TDPC054125


title: TDPC053843


title: TDPC053943


title: TDPC053730


title: TDPC061527


title: TDPC053713


title: TDPC053505


title: TDPC053449


title: TDPC053468


title: TDPC053228


title: TDPC060068


title: TDPC060086


title: TDPC052975


title: TDPC052962


title: TDPC053208


title: TDPC052727


title: TDPC053221


title: TDPC052698


title: TDPC053159


title: TDPC052801


title: TDPC060539


title: TDPC052636


title: TDPC054649


title: TDPC052596


title: TDPC052179


title: TDPC052084


title: TDPC051952


title: TDPC051709


title: TDPC051634


title: TDPC051286


title: TDPC051695


title: TDPC051147


title: TDPC051144


title: TDPC051499


title: TDPC050703


title: TDPC051134


title: TDPC050564


title: TDPC050546


title: TDPC050577


title: TDPC052502


title: TDPC050460


title: TDPC050568


title: TDPC050149


title: TDPC050242


title: TDPC050319


title: TDPC050582


title: TDPC050500


title: TDPC050335


title: TDPC050466


title: TDPC050070


title: TDPC050126


title: TDPC043988


title: TDPC043812


title: TDPC051009


title: TDPC043771


title: TDPC043145


title: TDPC043349


title: TDPC043075


title: TDPC052436


title: TDPC042882


title: TDPC042321


title: TDPC043545


title: TDPC042908


title: TDPC042130


title: TDPC041625


title: TDPC041654


title: TDPC041315


title: TDPC050004


title: TDPC041310


title: TDPC041354


title: TDPC042429


title: TDPC040880


title: TDPC040986


title: TDPC041132


title: TDPC040893


title: TDPC040831


title: TDPC041239


title: TDPC052281


title: TDPC041104


title: TDPC040561


title: TDPC040638


title: TDPC040383


title: TDPC040345


title: TDPC040585


title: TDPC040336


title: TDPC041419


title: TDPC040172


title: TDPC040164


title: TDPC040138


title: TDPC032050


title: TDPC032036


title: TDPC032056


title: TDPC031843


title: TDPC031932


title: TDPC031959


title: TDPC031808


title: TDPC040018


title: TDPC031517


title: TDPC040639


title: TDPC031617


title: TDPC031401


title: TDPC031049


title: TDPC031971


title: TDPC031265


title: TDPC031006


title: TDPC031188


title: TDPC030911


title: TDPC030950


title: TDPC030901


title: TDPC030863


title: TDPC030831


title: TDPC030808


title: TDPC030667


title: TDPC030541


title: TDPC030529


title: TDPC030374


title: TDPC030356


title: TDPC030348


title: TDPC030226


title: TDPC030161


title: TDPC030222


title: TDPC030986


title: TDPC022029


title: TDPC021533


title: TDPC021853


title: TDPC021444


title: TDPC021979


title: TDPC021970


title: TDPC021307


title: TDPC021921


title: TDPC021251


title: TDPC021787


title: TDPC020963


title: TDPC020808


title: TDPC020483


title: TDPC020630


title: TDPC020526


title: TDPC020411


title: TDPC020355


title: TDPC020537


title: TDPC020268


title: TDPC021469


title: TDPC020240


title: TDPC020894


title: TDPC020045


title: TDPC011922


title: TDPC012022


title: TDPC011731


title: TDPC011702


title: TDPC011698


title: TDPC020350


title: TDPC011600


title: TDPC011599


title: TDPC011570


title: TDPC011487


title: TDPC011142


title: TDPC011164


title: TDPC011061


title: TDPC011219


title: TDPC011213


title: TDPC010930


title: TDPC010674


title: TDPC010764


title: TDPC010605


title: TDPC010539


title: TDPC010432


title: TDPC010222


title: TDPC041221


title: TDPC010836


title: TDPC002700


title: TDPC010384


title: TDPC002384


title: TDPC011026


title: TDPC002701


title: TDPC001957


title: TDPC002052


title: TDPC000959


title: TDPC010727


title: TDPC001255


title: TDPC000870


title: TDPC000561


title: TDPC000467


title: TDPC000405


title: TDP94C362


title: TDPC000714


title: TDP94C240


title: TDPC002543


title: TDPC002323


title: TDP94C273


title: TDP94C100


title: TDP94C035


title: TDP94C079


title: TDP94C158


title: TDP93TDPC134


title: TDP93TDPC068


title: TDP94C022


title: SC, mstnb mutant - Uninjured - replicate 2

status: Public on Oct 20 2022

city: St. Louis

first: Mayssa

middle: H

last: Mokalled

state: MO

address: 4523 Clayton Ave, CB 8103

department: Developmental Biology

institute: Washington University in St. Louis

description: RNA from two mm SC section, located 4 mm caudal to the brainstem region, is extracted

data_processing:
Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome (Zv11) using Bowtie2,
then assembled and quantified using the Cufflinks and Cuffdiff algorithms.
Genes with log2(fold enrichment) between -1 and 1 or adjusted p-value ≥ 0.01 were considered insignificant.
Genome_build: Zv11
Supplementary_files_format_and_content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition.
Supplementary_files_format_and_content: Additionally, log2 Fold change is calculate between conditions as indicated in the file name.

organism: Danio rerio

source_name: Spinal cord

growth_protocol: Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 and 9 months of ~2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner, and 2 to 4 independent experiments were repeated using different clutches of animals.

extract_protocol:
Two mm SC sections, including the lesion site plus additional rostral and caudal tissue proximal to the lesion, were collected from mstnb mutants and wild-type siblings at 1 wpi. Uninjured mstnb mutants and wild-type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS (Clontech, cat# 740990)
TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired-end reading strategy.

treatment_protocol: Zebrafish were anaesthetized using MS-222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post-surgery. For sham injuries, animals were anaesthetized, and fine scissors were used to transect skin and muscle tissues without inducing SCI.

value: Spinal cord

tag: experiment

value: Uninjured

value: Control

value: mstnb mutant (-/-)


title: TDP93C287

value: male

value: White

value: Low


title: SC, mstnb wildtype - Uninjured - replicate 2

value: wildtype


title: TDPC000157

value: female

value: blood or bone marrow


title: SC, mstnb mutant - Uninjured - replicate 1


title: TDPC000118


title: TDPC002088

value: Adverse

value: Middle


title: SC, mstnb mutant - 1 wpi - replicate 2

description: RNA from two mm SC section flanking the injury site is extracted

value: Spinal cord (SC) injury

value: 1 week post injury


title: TDPC050809

value: Intermediate


title: TDP94TDPC302

value: Favorable


title: SC, mstnb mutant - 1 wpi - replicate 1


title: SC, mstnb wildtype - 1 wpi - replicate 2


title: SC, mstnb wildtype - Uninjured - replicate 1


title: DN4_snRNAseq

status: Public on Jul 28 2022

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

address: 660. S Euclid Ave., CB 8118

data_processing:
Fastq files was processed with cellranger v4.0 count using a custom pre-mrna reference GRCh38-2020-A.premrna
Filtered barcode-feaure matrix
snRNA-seq: cellranger count v4.0
snATAC-seq: cellranger-atac count v2.0
Genome_build: snRNA-seq: GRCh38-2020-A.premrna
Genome_build: snATAC-seq: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary_files_format_and_content: A total of 11 snRNA-seq libraries from this repository (1 control, 2 DKD), GSE13188213 (3 control, 3 DKD), and GSE151302 (2 control; samples 4 and 5) were counted with cellranger count v4.0 and a custom pre-mrna reference on GRCh38. A total of 13 snATAC-seq libraries from this repository (1 control, 7 dkd) and GSE151302 (5 control) were counted with cellranger-atac count v2.0 and refdata-cellranger-arc-GRCh38-2020-A-2.0.0.

source_name: Human Kidney Cortex - DN4

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snRNA-seq library (5' kit)
snRNA-seq
Nuclear isolation from bulk kidney cortex https://www.protocols.io/view/nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
10X genomics single cell gene expression OR single cell ATAC
snRNA-seq and snATAC-seq

value: M

value: Non-hispanic White

tag: egfr

tag: global glomerulosclerosis

tag: ifta


title: DN5_snRNAseq

source_name: Human Kidney Cortex - DN5

value: F

value: Moderate, 26 - 50%


title: Mouse, adult, female, knockout 66 [snATAC-Seq]

status: Public on Dec 27 2021

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

institute: University of Alabama at Birmingham

description: single nucleus ATAC -seq

data_processing:
CellRanger ATAC output files from filtered_peak_bc_matrix. For each sample (66, 67, 76, 77) there are peaaks.bed, singlecell.csv, and fragments.tsv.gz files.
These files were then further processed with Seurat v4.0.0 and Signacv1.2.0, and the data logNormalized, gene activity matrix generated, and scaled with the median nCount_RNA
Peaks.bed were converted to genomic ranges  with Signac and peak calling was performed with a unified set of peaks generated from these samples with Signac
Annotations were extracted from EnsDb.Musculculus.v79
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger ATAC output files from filtered_feature_bc_matrix. For each sample (66, 67, 76, 77) there are barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: fragments.tsv.gz
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: Indexed fragements
Supplementary_files_format_and_content: filtered_peak_bc_matrix.h5: Peak h5 files

source_name: kidney

extract_protocol:
The right kidney was excised, decapsulated, cut into 5 mm cubes and snap frozen. Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (cOmplete™ ULTRA tab; Sigma-Aldrich) . The frozen kidney cubes were placed in a sterile petri dish with 1 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors) and quickly minced.  The tissue was then homogenized with RNase-free, disposable pellet pestles and tubes (Fisher #12-141-368), and a hand held, Bel-Art™ Micro-Tube homogenizer (Wayne, NJ).  The homogenate was filtered through a 40 micron strainer (all strainers were purchase from pluriSelect Life Science).  The homogenate was moved to a sterile, RNase-free 15 ml tube with an additional 2 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors).  After a 5 min incubation on ice, the homogenate was filtered through a 40 micron strainer.  The subsequent homogenate was centrifuged at 500 g for 5 min at 4°C.  The pellet was resuspending in Nuclei EZ lysis buffer (plus 1 ml/ml of SUPERaseIN and RNAsin), incubated on ice for 5 min and centrifuged again.  The pellet was resuspended in 0.5 ml of  10X Genomics 1X nuclei suspension buffer, filtered through a 5 micron strainer, and nuclei immediately counted with a hemocytometer.
4000 nuclei per sample were loaded in the Chromium Next GEM Chip H Single Cell Kit and the DNA libraries generated with the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1

treatment_protocol: All mice were provided 2 mg/ml doxycycline in 2% sucrose water for 7 days, followed by 7-day washout before kidney excision.  Mice positive for PAX8-rtTA/LC-1 Cre would knock down HDAC1 and HDAC2.

value: Female

value: kidney, epithelial, HDAC1 and HDAC2 knockdown

value: kidney


title: SC, mstnb wildtype - 1 wpi - replicate 1

value: Spinal cord


title: TDP93TDPC014

value: male

value: White


title: Mouse, adult, male, knockout 76 [snATAC-Seq]

description: single nucleus ATAC -seq

value: Male


title: CSF-0709-D2-2_R1_GTAGAACG single cell from patient 6

status: Public on Aug 25 2021

city: Shanghai

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

country: China

institute: Tongji university

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_GTAGAACG

data_processing:
Sequenced reads were mapped to hg38 using the STAR (version 2.7; https://github.com/alexdobin/STAR) with the default parameters
Genome_build: hg38
Supplementary_files_format_and_content: gene count

source_name: cerebrospinal fluid

extract_protocol:
Antibody (CD45, CD3, CD19, BD Biosciences) and labeling dye for live cells (Calcein Blue AM, Life Technologies, CA) were used per manufacturer recommendations
Library for isolated single cell was generated by SMART-Seq2 method
SMART-Seq2 method

value: cerebrospinal fluid

tag: disease

value: CNSL-DLBCL


title: CSF-0709-D2-1_R1_CGTCTAAT single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-1_CGTCTAAT

tag: tissue


title: CSF-0709-D2-1_R1_GACAAACC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-1_GACAAACC


title: CSF-0709-D1-1_R1_TTCGGAAA single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_TTCGGAAA


title: CSF-0709-D1-1_R1_TGAATACC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_TGAATACC


title: CSF-0709-D1-1_R1_TGCGTAGG single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_TGCGTAGG


title: CSF-0709-D1-1_R1_GTGCATGA single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_GTGCATGA


title: CSF-0428-F2-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_TTCCGTTC


title: Mouse, adult, male, control 77 [snATAC-Seq]

description: single nucleus ATAC -seq

value: Control


title: CSF-0428-F2-2_combined_TGGAGCTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_TGGAGCTC


title: CSF-0709-D1-1_R1_TACTGGTA single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_TACTGGTA


title: CSF-0428-F2-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_GTTACAGG


title: CSF-0709-D1-1_R1_GTTGCCAC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D1-1_GTTGCCAC


title: CSF-0428-F2-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_AGCCACCA


title: CSF-0428-F2-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_ATACAGAC


title: CSF-0428-F2-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_TCAACGAC


title: CSF-0428-F2-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_GAGTCCTG


title: CSF-0709-D2-2_R1_GGTGGACT single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_GGTGGACT


title: CSF-0428-F2-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_CCAGTCCA


title: CSF-0428-F2-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_GGTAATCA


title: Mouse, adult, female, control 67 [snATAC-Seq]

description: single nucleus ATAC -seq


title: CSF-0428-F2-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_GGACCTTT


title: CSF-0428-F2-2_combined_AAGTGGCT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_AAGTGGCT


title: CSF-0428-F2-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_CGTCTAAT


title: CSF-0428-F2-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_GCACGTCA


title: CSF-0428-F2-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_CCTTCAAG


title: CSF-0428-F2-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_GGTGGACT


title: CSF-0428-F2-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_AGACTCGT


title: CSF-0428-F2-1_combined_ACCTCAGC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_ACCTCAGC


title: CSF-0428-F2-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_CACACTGA


title: CSF-0428-F2-2_combined_TAACTCCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-2_TAACTCCG


title: CSF-0428-F2-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_ATTTAGCG


title: CSF-0428-F2-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F2-1_AACGAGGT


title: CSF-0428-F1-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_GTTACAGG


title: CSF-0428-F1-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_GGTGGACT


title: CSF-0428-F1-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_TTCCGTTC


title: CSF-0428-F1-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_TCAACGAC


title: CSF-0428-F1-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_ATACAGAC


title: CSF-0428-F1-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_GAGTCCTG


title: CSF-0428-F1-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_AGACTCGT


title: CSF-0428-F1-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_ATTTAGCG


title: CSF-0428-F1-1_combined_ACCTCAGC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_ACCTCAGC


title: CSF-0428-F1-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_CCAGTCCA


title: CSF-0428-F1-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_GCACGTCA


title: CSF-0428-E2-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TTCCGTTC


title: CSF-0428-F1-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_AACGAGGT


title: CSF-0428-F1-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-2_AGCCACCA


title: CSF-0428-F1-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_GGTAATCA


title: CSF-0428-F1-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_CACACTGA


title: CSF-0428-E2-2_combined_TGTACCAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TGTACCAA


title: CSF-0428-F1-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_CGTCTAAT


title: CSF-0428-E2-2_combined_TGGAGCTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TGGAGCTC


title: CSF-0428-F1-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_CCTTCAAG


title: CSF-0428-E2-2_combined_TCTCACAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TCTCACAC


title: CSF-0428-E2-2_combined_TTACGGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TTACGGGT


title: CSF-0428-E2-2_combined_TCACCCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TCACCCGA


title: CSF-0428-E2-2_combined_TAACTCCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TAACTCCG


title: CSF-0428-E2-2_combined_GTCATTAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_GTCATTAG


title: CSF-0428-F1-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-F1-1_GGACCTTT


title: CSF-0428-E2-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_GTTACAGG


title: CSF-0428-E2-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_GGTGGACT


title: CSF-0428-E2-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_TCAACGAC


title: CSF-0428-E2-2_combined_GTAGAACG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_GTAGAACG


title: CSF-0428-E2-2_combined_CTTTGACA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_CTTTGACA


title: CSF-0428-E2-2_combined_CTGTCATT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_CTGTCATT


title: CSF-0428-E2-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_CCAGTCCA


title: CSF-0428-E2-2_combined_AGTTGTGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_AGTTGTGT


title: CSF-0428-E2-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_ATACAGAC


title: CSF-0428-E2-2_combined_ACGTATCC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_ACGTATCC


title: CSF-0428-E2-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_AGCCACCA


title: CSF-0428-E2-1_combined_TGAATACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_TGAATACC


title: CSF-0428-E2-1_combined_TGCGTAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_TGCGTAGG


title: CSF-0428-E2-1_combined_TACTGGTA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_TACTGGTA


title: CSF-0428-E2-2_combined_ACGATAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_ACGATAGG


title: CSF-0428-E2-1_combined_GTGCATGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GTGCATGA


title: CSF-0428-E2-1_combined_TTCGGAAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_TTCGGAAA


title: CSF-0428-E2-1_combined_GGATTGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GGATTGAC


title: CSF-0428-E2-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GGTAATCA


title: CSF-0428-E2-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GCACGTCA


title: CSF-0428-E2-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GGACCTTT


title: CSF-0428-E2-1_combined_CTGTACAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_CTGTACAA


title: CSF-0428-E2-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_GAGTCCTG


title: CSF-0428-E2-1_combined_GACAAACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GACAAACC


title: CSF-0428-E2-2_combined_CGCAAAGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_CGCAAAGT


title: CSF-0428-E2-1_combined_GATGTCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GATGTCGA


title: CSF-0428-E2-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_CACACTGA


title: CSF-0428-E2-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_CGTCTAAT


title: CSF-0428-E2-2_combined_AAGTGGCT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_AAGTGGCT


title: CSF-0428-E2-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_ATTTAGCG


title: CSF-0428-E2-1_combined_AGCTCCTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_AGCTCCTT


title: CSF-0428-E2-1_combined_GTTGCCAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_GTTGCCAC


title: CSF-0428-E2-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-2_AGACTCGT


title: CSF-0428-E2-1_combined_ACTGTTTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_ACTGTTTG


title: CSF-0428-E2-1_combined_AAGCACAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_AAGCACAT


title: CSF-0428-E2-1_combined_ACACCGTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_ACACCGTG


title: CSF-0428-E2-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_AACGAGGT


title: CSF-0428-E1-2_combined_TGTACCAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TGTACCAA


title: CSF-0428-E1-2_combined_TTACGGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TTACGGGT


title: CSF-0428-E1-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TTCCGTTC


title: CSF-0428-E2-1_combined_ACCTCAGC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_ACCTCAGC


title: CSF-0428-E1-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_GGTGGACT


title: CSF-0428-E1-2_combined_TAACTCCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TAACTCCG


title: CSF-0428-E1-2_combined_GTCATTAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_GTCATTAG


title: CSF-0428-E1-2_combined_CTTTGACA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_CTTTGACA


title: CSF-0428-E1-2_combined_TGGAGCTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TGGAGCTC


title: CSF-0428-E1-2_combined_TCACCCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TCACCCGA


title: CSF-0428-E2-1_combined_CACAGCAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_CACAGCAT


title: CSF-0428-E1-2_combined_CGCAAAGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_CGCAAAGT


title: CSF-0428-E1-2_combined_TCTCACAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TCTCACAC


title: CSF-0428-E1-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_ATACAGAC


title: CSF-0428-E2-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E2-1_CCTTCAAG


title: CSF-0428-E1-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_TCAACGAC


title: CSF-0428-E1-2_combined_GTAGAACG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_GTAGAACG


title: CSF-0428-E1-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_GAGTCCTG


title: CSF-0428-E1-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_AGCCACCA


title: CSF-0428-E1-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_AGACTCGT


title: CSF-0428-E1-2_combined_ACGTATCC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_ACGTATCC


title: CSF-0428-E1-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_GTTACAGG


title: CSF-0428-E1-2_combined_CTGTCATT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_CTGTCATT


title: CSF-0428-E1-2_combined_ACGATAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_ACGATAGG


title: CSF-0428-E1-1_combined_TTCGGAAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_TTCGGAAA


title: CSF-0428-E1-2_combined_AGTTGTGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_AGTTGTGT


title: CSF-0428-E1-1_combined_TGAATACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_TGAATACC


title: CSF-0428-E1-1_combined_TGCGTAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_TGCGTAGG


title: CSF-0428-E1-1_combined_TACTGGTA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_TACTGGTA


title: CSF-0428-E1-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_CCAGTCCA


title: CSF-0428-E1-1_combined_GTGCATGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GTGCATGA


title: CSF-0428-E1-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GGTAATCA


title: CSF-0428-E1-1_combined_CTGTACAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_CTGTACAA


title: CSF-0428-E1-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GCACGTCA


title: CSF-0428-E1-1_combined_GACAAACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GACAAACC


title: CSF-0428-E1-1_combined_GATGTCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GATGTCGA


title: CSF-0428-E1-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GGACCTTT


title: CSF-0428-E1-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_CGTCTAAT


title: CSF-0428-E1-1_combined_GGATTGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GGATTGAC


title: CSF-0428-E1-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_CCTTCAAG


title: CSF-0428-E1-1_combined_CACAGCAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_CACAGCAT


title: CSF-0428-E1-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_CACACTGA


title: CSF-0428-E1-1_combined_ACTGTTTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_ACTGTTTG


title: CSF-0428-E1-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_ATTTAGCG


title: CSF-0428-E1-1_combined_ACACCGTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_ACACCGTG


title: CSF-0428-E1-1_combined_AGCTCCTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_AGCTCCTT


title: CSF-0428-E1-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_AACGAGGT


title: CSF-0428-D2-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TTCCGTTC


title: CSF-0428-E1-1_combined_ACCTCAGC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_ACCTCAGC


title: CSF-0428-E1-2_combined_AAGTGGCT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-2_AAGTGGCT


title: CSF-0428-D2-2_combined_TTACGGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TTACGGGT


title: CSF-0428-D2-2_combined_TGTACCAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TGTACCAA


title: CSF-0428-D2-2_combined_TGGAGCTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TGGAGCTC


title: CSF-0428-E1-1_combined_GTTGCCAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_GTTGCCAC


title: CSF-0428-D2-2_combined_TCTCACAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TCTCACAC


title: CSF-0428-D2-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TCAACGAC


title: CSF-0428-D2-2_combined_TCACCCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TCACCCGA


title: CSF-0428-D2-2_combined_TAACTCCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_TAACTCCG


title: CSF-0428-D2-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_GTTACAGG


title: CSF-0428-D2-2_combined_GTCATTAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_GTCATTAG


title: CSF-0428-D2-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_GGTGGACT


title: CSF-0428-D2-2_combined_CTTTGACA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_CTTTGACA


title: CSF-0428-D2-2_combined_CGCAAAGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_CGCAAAGT


title: CSF-0428-D2-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_CCAGTCCA


title: CSF-0428-D2-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_GAGTCCTG


title: CSF-0428-E1-1_combined_AAGCACAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-E1-1_AAGCACAT


title: CSF-0428-D2-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_ATACAGAC


title: CSF-0428-D2-2_combined_CTGTCATT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_CTGTCATT


title: CSF-0428-D2-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_AGACTCGT


title: CSF-0428-D2-2_combined_AAGTGGCT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_AAGTGGCT


title: CSF-0428-D2-2_combined_ACGATAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_ACGATAGG


title: CSF-0428-D2-1_combined_TTCGGAAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_TTCGGAAA


title: CSF-0428-D2-2_combined_ACGTATCC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_ACGTATCC


title: CSF-0428-D2-2_combined_AGTTGTGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_AGTTGTGT


title: CSF-0428-D2-1_combined_TGCGTAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_TGCGTAGG


title: CSF-0428-D2-1_combined_GTGCATGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GTGCATGA


title: CSF-0428-D2-1_combined_GGATTGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GGATTGAC


title: CSF-0428-D2-1_combined_GTTGCCAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GTTGCCAC


title: CSF-0428-D2-1_combined_GATGTCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GATGTCGA


title: CSF-0428-D2-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GCACGTCA


title: CSF-0428-D2-1_combined_GACAAACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GACAAACC


title: CSF-0428-D2-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GGTAATCA


title: CSF-0428-D2-2_combined_GTAGAACG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_GTAGAACG


title: CSF-0428-D2-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_GGACCTTT


title: CSF-0428-D2-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-2_AGCCACCA


title: CSF-0428-D2-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_CGTCTAAT


title: CSF-0428-D2-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_CCTTCAAG


title: CSF-0428-D2-1_combined_CTGTACAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_CTGTACAA


title: CSF-0428-D2-1_combined_CACAGCAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_CACAGCAT


title: CSF-0428-D2-1_combined_TGAATACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_TGAATACC


title: CSF-0428-D2-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_CACACTGA


title: CSF-0428-D2-1_combined_AGCTCCTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_AGCTCCTT


title: CSF-0428-D2-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_ATTTAGCG


title: CSF-0428-D2-1_combined_ACCTCAGC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_ACCTCAGC


title: CSF-0428-D2-1_combined_ACACCGTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_ACACCGTG


title: CSF-0428-D2-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_AACGAGGT


title: CSF-0428-D2-1_combined_TACTGGTA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_TACTGGTA


title: CSF-0428-D1-2_combined_TGTACCAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TGTACCAA


title: CSF-0428-D1-2_combined_TGGAGCTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TGGAGCTC


title: CSF-0428-D1-2_combined_TCTCACAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TCTCACAC


title: CSF-0428-D1-2_combined_TCACCCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TCACCCGA


title: CSF-0428-D1-2_combined_TCAACGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TCAACGAC


title: CSF-0428-D1-2_combined_TTACGGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TTACGGGT


title: CSF-0428-D1-2_combined_GTTACAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_GTTACAGG


title: CSF-0428-D1-2_combined_CTTTGACA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_CTTTGACA


title: CSF-0428-D1-2_combined_GTAGAACG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_GTAGAACG


title: CSF-0428-D1-2_combined_CGCAAAGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_CGCAAAGT


title: CSF-0428-D1-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TTCCGTTC


title: CSF-0428-D1-2_combined_GGTGGACT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_GGTGGACT


title: CSF-0428-D1-2_combined_CTGTCATT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_CTGTCATT


title: CSF-0428-D1-2_combined_GAGTCCTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_GAGTCCTG


title: CSF-0428-D1-2_combined_GTCATTAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_GTCATTAG


title: CSF-0428-D1-2_combined_TAACTCCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_TAACTCCG


title: CSF-0428-D1-2_combined_ATACAGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_ATACAGAC


title: CSF-0428-D1-2_combined_AGTTGTGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_AGTTGTGT


title: CSF-0428-D1-2_combined_AGCCACCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_AGCCACCA


title: CSF-0428-D1-2_combined_CCAGTCCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_CCAGTCCA


title: CSF-0428-D2-1_combined_ACTGTTTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_ACTGTTTG


title: CSF-0428-D2-1_combined_AAGCACAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D2-1_AAGCACAT


title: CSF-0428-D1-2_combined_AGACTCGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_AGACTCGT


title: CSF-0428-D1-2_combined_ACGATAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_ACGATAGG


title: CSF-0428-D1-1_combined_TGCGTAGG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_TGCGTAGG


title: CSF-0428-D1-1_combined_TTCGGAAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_TTCGGAAA


title: CSF-0428-D1-2_combined_AAGTGGCT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_AAGTGGCT


title: CSF-0428-D1-2_combined_ACGTATCC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-2_ACGTATCC


title: CSF-0428-D1-1_combined_TACTGGTA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_TACTGGTA


title: CSF-0428-D1-1_combined_GGTAATCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GGTAATCA


title: CSF-0428-D1-1_combined_TGAATACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_TGAATACC


title: CSF-0428-D1-1_combined_GGATTGAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GGATTGAC


title: CSF-0428-D1-1_combined_GTTGCCAC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GTTGCCAC


title: CSF-0428-D1-1_combined_GTGCATGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GTGCATGA


title: CSF-0428-D1-1_combined_GGACCTTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GGACCTTT


title: CSF-0428-D1-1_combined_GCACGTCA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GCACGTCA


title: CSF-0428-D1-1_combined_CTGTACAA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_CTGTACAA


title: CSF-0428-D1-1_combined_GACAAACC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GACAAACC


title: CSF-0428-D1-1_combined_CGTCTAAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_CGTCTAAT


title: CSF-0428-D1-1_combined_GATGTCGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_GATGTCGA


title: CSF-0428-D1-1_combined_CCTTCAAG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_CCTTCAAG


title: CSF-0428-D1-1_combined_CACAGCAT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_CACAGCAT


title: CSF-0428-D1-1_combined_CACACTGA single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_CACACTGA


title: CSF-0428-D1-1_combined_ATTTAGCG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_ATTTAGCG


title: CSF-0428-D1-1_combined_ACTGTTTG single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_ACTGTTTG


title: CSF-0428-C2-2_combined_TTCCGTTC single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-C2-2_TTCCGTTC


title: CSF-0428-C2-2_combined_TTACGGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-C2-2_TTACGGGT


title: CSF-0428-D1-1_combined_AACGAGGT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_AACGAGGT


title: CSF-0428-D1-1_combined_AGCTCCTT single cell from patient 1

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P1.csv
CSF-0428-D1-1_AGCTCCTT


title: CSF-0709-D2-2_combined_TTCCGTTC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_TTCCGTTC


title: CSF-0709-D2-2_combined_TGGAGCTC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_TGGAGCTC


title: CSF-0709-D2-2_combined_TCTCACAC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_TCTCACAC


title: CSF-0709-D2-2_combined_TCAACGAC single cell from patient 6

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P6.csv
CSF-0709-D2-2_TCAACGAC